The town was established in 1858, the 50th anniversary of the Spanish victory against France in the Battle of Bailén that was fought in 1808 during the Peninsular War.

It was founded by virtue of a decree issued on August 28, 1857, by Archbishop Fray Aranguren, OSA, of the Archdiocese of Manila.

The American civil government, from 1899 to 1901, reduced the number of towns to facilitate the military policy of concentrating the civilian population of the poblaciones.

4346, the town's name, Bailen, was changed to General Emilio Aguinaldo, in honor of the first Philippine president, who died the year prior.

The Cavite Provincial Board unanimously approved Committee Report 118-2012, renaming General Emilio Aguinaldo, during the 95th Regular Session.